Shake quicktime woes

We're having a nightmare of a time rendering out quicktimes from Shake at 23.98 using the Black Magic Codec and using them in After Effects. Any Black Magic quicktime coming out of Shake and imported into After Effects is read with a doubled up first frame and missing last frame.
We've tried numerous image sequences of all different formats with the same results.
Other frame rates don't seem to have that problem. Only 23.98
Also Shake isn't embedding any of the usual quicktime fps, data rate, current time, duration, etc info in the quicktime movie inspector.
Any insight would be appreciated.

Well the issue is we need to use command line Shake because we're writing a tool that automatically generates Slates, creates a quicktime, sends it to our dailies folder and updates our production management system.

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